Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CSTF2

Cell type

Cell type Class
Pancreas
Cell type
PDAC
NA
NA

Attributes by original data submitter

Sample

source_name
Bo103, PDAC
cell line
Bo103, PDAC
treatment
SN38+JQ1
cell type
Pancreatic tumor patient-derived cells
chip antibody
Cstf64 (Bethyl Laboratories, #A301092A)
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM6473100
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde (Thermo Fisher, 28906) for 5 min. Cross-linking was stopped by the addition of glycine (125 mM) and cells were washed twice with cold PBS. After harvesting cells by scraping, the pellet was washed once with PBS plus 0.5% BSA and resuspended in RIPA buffer to a final concentration of 1x10^7 cells/ml. Samples were sonicated with a Bandelin probe sonicator to produce chromatin fragments of 400 bps on average. DNA from ChIP was quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher, Q33230). Sequencing libraries were created according to the ThruPLEX DNA-seq kit protocol (Takara, R400676). Size selection was performed in the range of 200-700bp with AMPure XP beads (Beckman, A63880) and confirmed using the Agilent High Sensitivity DNA Kit (Agilent, 5067-4626) on the Agilent 2100 Bioanalyzer. Libraries were pooled and sequenced using the NextSeq 500/550 High Output Kit v2.5 (Illumina, 20024906). The sequencing run was Single End and Dual Index with 75 bp reads.

Sequencing Platform

instrument_model
NextSeq 550

hg38

Number of total reads
34533884
Reads aligned (%)
84.0
Duplicates removed (%)
27.9
Number of peaks
876 (qval < 1E-05)

hg19

Number of total reads
34533884
Reads aligned (%)
83.4
Duplicates removed (%)
29.1
Number of peaks
920 (qval < 1E-05)

Base call quality data from DBCLS SRA